Ok, so I am a guitar player, not a tech. I know how to set up my guitars, and do some basic maintenance and tweaks.
But I bought a used Jackson electric guitar from a pawn shop here in Costa Rica, and came across a problem I've never seen before. The low E and A strings, on the first 3 frets, cannot be played regularly because the frets are so high, that if I push the string down to the fretboard, it raises the pitch almost half a step! If I play them very lightly, and right on the fret, I can muddle through. But playing chords with the low E string on the first 3 frets is impossible.
The rest of the neck is fine...but this problem confounds me. I hesitate to take sandpaper to the frets because I don't know if that will really solve the problem; and I've never done that before. The frets are like new, and very clean and without any visible wear.
Should I just do the obvious, and sand the frets down?

I'd have to hold the guitar myself to actually be able to assess. But it sounds like the neck has warped a bit due to temperature. If you've properly adjusted the truss rod, the nut, and the bridge then honestly the only work around I could think of right now would be to file down the frets that are too high.

What you're describing is a bit strange though and might actually have been an intended effect. A lot of asian stringed instruments have frets that are incredibly high so that you can do funky sitar-like bends.

The instrument might also just have been poorly crafted.

However the most likely explanation is that the neck warped to due temperature.

I do not agree with OPs advice. I have a neck presently that has similar issues at two different spots. The neck is bound which complicates the repair FOR ME. I would suggest that you refer to these two articles BEFORE you attempt to fix the high frets :

These articles discusses the ins & outs of contouring frets. The tools are expensive - I have a six each set of 3 each fret crowning files and 3 each of nut slotting files that I bought in 1978 for $80. The repair is something that requires a patiently accurate use of the tools required to accomplish the repair.

I would compare the quote that a luthier would bid the repair at versus the value of the instrument - reverb.com has a database of prices on instruments. Here's the link :

I am stating all of this because I have been in similar situations many times over the 40+ years that I have spent buying, repairing and reselling instruments. I have enough luthier tools that will allow me to accomplish work on electric guitars and some tasks on acoustics.

The better the condition of frets on a guitar then the EASIER AND BETTER it will respond to a players fretting abilities while playing.

I apologize IF I came across too strongly. The Truth is a beootch sometimes......

The truss rod was adjusted incorrectly as it was loose and was not doing it's job. Correcting this issue, leveled the fret-board perfectly and the frets were the issue now, so I began the next steps.

It was a long process to get the 24 frets leveled, crowned and polished, 38hrs. of loving labor is how much time I dedicated to this job, total. Using a cordless Dremel Tool to polish the frets after crowning was a time saver and the only issue I had was discovering how to get the jeweler's rouge loaded into the small buffing attachment that I was using. The answer involved using the Dremel's - High/Low - and using the Low speed as a starting point cured the problem of loosing the polishing compound from the buffing wheel.

The neck ended up being one of the finest repairs of this nature that I have ever completed. After reattaching it to the body and setting up the guitar, I was more than satisfied. It plays extremely well and comfortable. There's no problems with the guitar! Even though I used these Dunlop strings :

The instrument plays exceptionally! I am delighted that the work involved yielded an instrument that is so comfortable to play. I learned some valued lessons that will make future projects like this one easier to accomplish.

It's not uncommon for a neck to warp, so you want to check the fretboard to see if it's straight. After you have straightened the truss rod, get a notched straight edge and check to see if the fretboard itself is straight. After all, if the fretboard isn't flat, the frets probably won't be either.

Then take a straight edge across the frets themselves to see if they are flat. Sometimes frets come loose or just aren't installed right to begin with. Changes are this is your probably. You'll need to level, dress, and crown the frets. Here's a guide on how to do that.